Thanks Nigel.
The CIF files generated by SKETCHER in ccp4i work fine in both
phenix.refine and refmac, but seems they don't work in
phenix.autobuild....(they should work the same right?)
I am not sure why, but I will try what you suggested. Thank you so much again!
Matt
Matt
>* 1. AutoBuild Wizard will use phenix.elbow to generate geometries for
*>* any ligands that are not recognized, but how can I find out which
*>* ligands that can actually be recognized by phenix? Or to be save, we
*>* better run elbow to generate the libraries for every single ligands?
*There are a number of tools available.
phenix.pdbtools file.pdb
will tell you if a PDB file has non-recognised ligands.
phenix.elbow --do-all model.pdb
will calculate all the ligands in the PDB file.
phenix.ready_set model.pdb
will calculate all the ligands and check that the atom names are
correct. It also adds hydrogens among other things.
>* 2. eLBOW can automatically add hydrogens to the input molecules if
*>* there are less than a quarter of the possible hydrogens, however this
*>* command doesn't work: phenix.elbow input_file.pdb
*>* --add-hydrogens=True, and I can't find this option under the elbow manual?
*>* And actually I would like to remove those hydrogens so it should be
*>* "add-hydrogens=false"? I am now using phenix-1.3-rc2.
*
To get an absolute list of the options you can
phenix.elbow --help
The --add-hydrogens options overwrites the automatic choice by eLBOW.
If you don't want the hydrogens in your PDB and CIF files use
--write-hydrogens=False. This arises because the internal
representation must have the hydrogens for accurate geometries and
restraints.
Nigel
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty at LBL.gov
<http://www.phenix-online.org/mailman/listinfo/phenixbb>
Web : CCI.LBL.gov
--
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Matthew LH Chu
PhD Student
School of Pharmacy and Pharmaceutical Sciences
University of Manchester
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